BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform

Farrell, Colin; Thompson, Michael J.; Tosevska, Anela; Oyetunde, Adewale; Pellegrini, Matteo

doi:10.1101/2020.10.06.328559

Cited by 11 publications

(12 citation statements)

References 21 publications

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“…FastQC (v0.11.8) was used to assess the quality of the raw reads and adapter‐trimmed reads (cutadapt, version 2.5). Reads were mapped to the GRCm38 RRBS genome using BSBolt v0.1.2 (https://github.com/NuttyLogic/BSBolt) (Farrell et al, 2021). Methylation was called and the CpG methylation matrix was assembled for CpG sites common to all samples and covered by more than 10 reads.…”

Section: Methodsmentioning

confidence: 99%

Tick tock, tick tock: Mouse culture and tissue aging captured by an epigenetic clock

et al. 2022

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Aging is associated with dramatic changes to DNA methylation (DNAm), although the causes and consequences of such alterations are unknown. Our ability to experimentally uncover mechanisms of epigenetic aging will be greatly enhanced by our ability to study and manipulate these changes using in vitro models. However, it remains unclear whether the changes elicited by cells in culture can serve as a model of what is observed in aging tissues in vivo. To test this, we serially passaged mouse embryonic fibroblasts (MEFs) and assessed changes in DNAm at each time point via reduced representation bisulfite sequencing. By developing a measure that tracked cellular aging in vitro, we tested whether it tracked physiological aging in various mouse tissues and whether anti-aging interventions modulate this measure. Our measure, termed CultureAGE, was shown to strongly increase with age when examined in multiple tissues (liver, lung, kidney, blood, and adipose). As a control, we confirmed that the measure was not a marker of cellular senescence, suggesting that it reflects a distinct yet progressive cellular aging phenomena that can be induced in vitro. Furthermore, we demonstrated slower epigenetic aging in animals undergoing caloric restriction and a resetting of our measure in lung and kidney fibroblasts when re-programmed to iPSCs. Enrichment and clustering analysis implicated EED and Polycomb group (PcG) factors as potentially important chromatin regulators in translational culture aging phenotypes. Overall, this study supports the concept that physiologically relevant aging changes can be induced in vitro and used to uncover mechanistic insights into epigenetic aging.

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Section: Methodsmentioning

confidence: 99%

Tick tock, tick tock: Mouse culture and tissue aging captured by an epigenetic clock

et al. 2022

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“…The primer and probe sequences used for targeted bisulfite sequencing (both for validation of RRBS-derived CpGs and for Framingham Heart Study significant CpGs) are included as a Supplementary Excel File . Following biotinylated probe pull down with streptavidin coated magnetic beads, the pooled samples underwent bisulfite conversion, PCR amplification, sequencing and alignment to human reference genome hg38 followed by counting methylated and unmethylated CpGs using BSBolt ( 27 ).…”

Section: Methodsmentioning

confidence: 99%

DNA Methylation-Based Prediction of Post-operative Atrial Fibrillation

Fischer

Mahajan

Cabaj

et al. 2022

Front. Cardiovasc. Med.

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BackgroundAtrial fibrillation (AF) is the most common sustained cardiac arrhythmia and post-operative atrial fibrillation (POAF) is a major healthcare burden, contributing to an increased risk of stroke, kidney failure, heart attack and death. Genetic studies have identified associations with AF, but no molecular diagnostic exists to predict POAF based on pre-operative measurements. Such a tool would be of great value for perioperative planning to improve patient care and reduce healthcare costs. In this pilot study of epigenetic precision medicine in the perioperative period, we carried out bisulfite sequencing to measure DNA methylation status in blood collected from patients prior to cardiac surgery to identify biosignatures of POAF.MethodsWe enrolled 221 patients undergoing cardiac surgery in this prospective observational study. DNA methylation measurements were obtained from blood samples drawn from awake patients prior to surgery. After controlling for clinical and methylation covariates, we analyzed DNA methylation loci in the discovery cohort of 110 patients for association with POAF. We also constructed predictive models for POAF using clinical and DNA methylation data. We subsequently performed targeted analyses of a separate cohort of 101 cardiac surgical patients to measure the methylation status solely of significant methylation loci in the discovery cohort.ResultsA total of 47 patients in the discovery cohort (42.7%) and 43 patients in the validation cohort (42.6%) developed POAF. We identified 12 CpGs that were statistically significant in the discovery cohort after correcting for multiple hypothesis testing. Of these sites, 6 were amenable to targeted bisulfite sequencing and chr16:24640902 was statistically significant in the validation cohort. In addition, the methylation POAF prediction model had an AUC of 0.79 in the validation cohort.ConclusionsWe have identified DNA methylation biomarkers that can predict future occurrence of POAF associated with cardiac surgery. This research demonstrates the use of precision medicine to develop models combining epigenomic and clinical data to predict disease.

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“…We utilized the BSBolt software (Farrell et al, 2020) package from https://github.com/NuttyLogic/BSBolt to perform the alignments. For each species' genome sequence, BSBolt creates an 'in silico' bisulfite-treated version of the genome.…”

Section: Mappability Approach 1: Bsboltmentioning

confidence: 99%

A mammalian methylation array for profiling methylation levels at conserved sequences

Arneson

Haghani

Thompson³

et al. 2021

Preprint

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SUMMARYInfinium methylation arrays are widely used to robustly measure methylation of DNA in humans. However, such arrays are not available for the vast majority of non-human mammals. Moreover, even if species-specific arrays were available, probe differences between them would confound cross-species comparisons. To address these challenges, we developed the Mammalian Methylation Array, a single custom Infinium array that measures cytosine methylation levels of over 35 thousand CpG sites that are well conserved across species within the mammalian class. By design, the probes on the array tolerate cross-species mutations. To design the array, we developed the Conserved Methylation Array Probe Selector (CMAPS) algorithm, which takes as input a multi-species sequence alignment and probe design constraints. A greedy search algorithm was used to identify oligonucleotide sequences (probes) with high coverage across different mammalian species. We annotate the probes on the array with respect to genes in 159 different species and provide details on the sequence context including CpG island status and chromatin states. Our calibration experiments demonstrate the high fidelity of this array in humans, rats, and mice. The mammalian methylation array has several strengths: it applies to all mammalian species even those that have not yet been sequenced, it provides deep coverage of specific cytosines facilitating the development of highly robust epigenetic biomarkers, and it covers highly conserved CpGs which greatly increases the probability that biological insights gained in one species will readily translate to others. The mammalian methylation array is expected to find many applications in preclinical studies, comparative biology, and epigenetic studies of aging and development.

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BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform

Cited by 11 publications

References 21 publications

Tick tock, tick tock: Mouse culture and tissue aging captured by an epigenetic clock

Tick tock, tick tock: Mouse culture and tissue aging captured by an epigenetic clock

DNA Methylation-Based Prediction of Post-operative Atrial Fibrillation

A mammalian methylation array for profiling methylation levels at conserved sequences

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